Re: [phenixbb] phenix.phaser params.eff labin problem

Thanks a lot Nat! I tried exactly what you suggested. Still it returned me could not find the labels. I also tried labin = "FP,SIGFP" and labin="FP, SIGFP" and other possiblities with or withour space in between. They all returned me could not find the label FP, SIGFP. Should I give the keyword in capital letters. Or may be I should try other format input file? I do not care about anomalous signal in this data, because I will just use MR_AUTO model in phenix.phaser. Any other ideas would be greatly appreciated. Thanks again for your time. Best regards, GP On Tue, Jul 19, 2011 at 5:47 PM, Nathaniel Echols wrote:

On Tue, Jul 19, 2011 at 3:13 AM, G P wrote:

...

I am now writing a script for phenix.phaser. In the input file params.eff there is a keyword labin which corresponds to the labels inside input mtz files. The important columns in my ccp4 mtz file are FP, SIGFP. I edit the line of labin as: labin F=FP SIGF=SIGFP when running the script, it returns me: Syntax error: expected "=", found "F" (file "params.eff", line 9) So, I changed it like: labin=FP SIGFP when running, it gave me the message: Sorry: Couldn't find array FP SIGP in file I also tried: labin="FP" or labin = "FP SIGFP" or labin="labin F=FP" and so on. With nothing it can find the right columns. My mtz file should be not problem, I checked with mtzdmp, the columns FP and SIGFP were there and with phenix GUI this file works well. Would someone know exactly how to edit this line in params.eff?

labin="FP,SIGFP"

The syntax used for these parameter files is much different from the CCP4 keyword input - this was necessary for incorporating Phaser into the Phenix GUI. Among other things, we specify data labels in groups, and internally "FP,SIGFP" is a single data structure containing both the amplitudes and sigmas. FYI, unlike the CCP4 version, with phenix.phaser you can use any type of data as input, so an anomalous Scalepack file will work too. (Of course you still need to know what labels to use - someday I intend to make the setup more automatic on the command line.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb